Via Good to the Grain by Kim Boyce.
2 Tbsp. butter, melted, for the bowl and baking sheets
1 package active dry yeast
1 tbsp. honey
1 cup rye flour
2 1/2 cups all-purpose flour
1 tbsp. kosher salt
1/2 cup baking soda
Coarse sea salt
Measure the yeast into a large bowl. Heat 1.5 cups of water in a saucepan till warm to the touch, about 100 degrees F, and pour over yeast. Add the honey and stir to combine. (Make sure the yeast starts to expand and bubble to make sure it's active). Add the flours and salt, and stir again.
Dump the sticky dough onto a floured surface and knead. Add up to 1/2 cup all-purpose flour as needed until the dough is tacky but not sticky. Knead for about 12 minutes, until the dough is soft and supple.
Lightly brush a large bowl with the melted butter. Move the dough into the owl, and cover with a warm wet towel (so dough doesn't dry out) and let rise about 1.5 hours until doubled in size.
While the dough is rising, make sure your oven is turned on to 450 degrees F, and that the two racks are at the top and bottom thirds of the oven. Brush two baking sheets generously with butter.
Once the dough is doubled, gently pour it from the bowl onto a lightly floured surface. Cut the dough into 12 equal pieces. One at a time (leave the remaining pieces covered by the wet towel meanwhile), roll out each piece of dough into the shape of a long snake, about 15-17 inches long. Don't flour the surface as your roll; the slight stickiness lets you roll the dough evenly and quickly.
To make the pretzel shape: take both ends of the snake-shape (leaving the center on the counter) and meet in the middle, and switch places in the hands (so the left side is now in right hand, and right side now in left hand). Bring the ends back down and make sure it has the curves of a normal pretzel shape, and gently press back down onto the sides of the center of the snake-shaped roll. Place pretzel on one of the baking sheets. Continue until you are finished with all the dough and pretzels, and let rise additional 15-20 minutes.
Meanwhile, for the bath, fill a large pot with ten cups of water, and bring to a boil. Once the pretzels have risen for the 20 minutes and the water is boiling, add the baking soda to the water. Place 2-3 pretzels into the pot, (depending on size of pot, you don't want the pretzels to touch), and boil each side of the pretzel for 30 seconds, then use a straining spoon to lift the pretzels out and back onto the baking sheets, (tapping gently with a towel or against pot to remove excess water). Repeat for all pretzels, and sprinkle liberally with salt while still moist.
Place the baking sheets with pretzels in the oven and bake 15-18 minutes, rotating sheets halfway through. The pretzels should be a dark mahogany color. Transfer to a rack to cool, and are best eaten warm, ideally within the hour and with mustard.